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Golden BAM emits CIGARs ending in a deletion, which overstate the reference span

Status: Open.

#339 In ncsa/NEAT;

· joshfactorial opened on Aug 29, 2026

apply_errors quality accounting has compensating off-by-ones, and blocks the remaining half of #335

Status: Open.

#337 In ncsa/NEAT;

· joshfactorial opened on Aug 29, 2026

research single cell simulation

Status: Open.

#320 In ncsa/NEAT;

· joshfactorial opened on Jun 26, 2026

look into allelic dropout

Status: Open.

#319 In ncsa/NEAT;

· joshfactorial opened on Jun 26, 2026

look into amplification bias

Status: Open.

#318 In ncsa/NEAT;

· joshfactorial opened on Jun 26, 2026

model_sequencing_error: derive error transition/indel/insertion params from input FASTQ

Status: Open.

#295 In ncsa/NEAT;

· joshfactorial opened on May 19, 2026

Integrate sub functions

Status: Open.

#290 In ncsa/NEAT;

· joshfactorial opened on May 19, 2026

specify an allele frequency

Status: Open.

#289 In ncsa/NEAT;

· joshfactorial opened on May 19, 2026

CNV addition

Status: Open.

#288 In ncsa/NEAT;

· joshfactorial opened on May 19, 2026

Copy number scripts

Status: Open.

#226 In ncsa/NEAT;

· keshav-gandhi opened on Dec 12, 2025